Mr. Lincoln's paramount goal was the preservation of the Union. I believe that in his mind this objective overrode any concern for what the fallout might be. (Loss of civil liberties, massive loss of life, etc.)

Mr. Lincoln believed that he had to assume emergency powers in order to prevent the government from coming apart at the seams. In his mind, he was the one person who was in a position to take the actions necessary to prevent the collapse of the nation. In this situation, observing legal niceties was not a high priority. He was quite willing to do anything that he thought was necessary to preserve the Union. I don't think it mattered to him that millions of people no longer wished to be his fellow citizens.

I've said a number of times that it is difficult for me in the 21st Century to fully understand the mindsets of 19th Century men. One reason often given by northerners for their determination to preserve the Union was that if the country split up, it would somehow mean that the world's great democratic experiment had failed, and that men couldn't govern themselves properly in a nation of laws. (To me, the idea that the U.S. was somehow representative of all of mankind was a pretentious view to take.)

The northerners had the option of letting the southerners go in peace. But they preferred a war to accepting secession. (Perhaps they feared that the northern states would fragment themselves in the future).

To me, the idea that you can prove that you are a nation of laws by disregarding your own laws and conducting a war that kills hundreds of thousands does not seem consistent. The idea of how forcing the unwilling to remain a part of a democracy (Or in the case of the U.S. more properly described as a : "Representative republic") at the point of a bayonet proves its viability still eludes me.